scverse

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52 repositories

scvi-tools
Public
Deep probabilistic analysis of single-cell and spatial omics data
deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•375•1.3k•44•15•Updated Feb 10, 2025Feb 10, 2025
pertpy
Public
Perturbation Analysis in the scverse ecosystem.
single-cell perturbation scverse
Python
•
MIT License
•25•151•34•2•Updated Feb 7, 2025Feb 7, 2025
anndataR
Public
AnnData interoperability in R
anndata h5ad
R
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Other
•11•69•18•3•Updated Feb 7, 2025Feb 7, 2025
rapids_singlecell
Public
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
bioinformatics gpu single-cell anndata scverse
Python
•
MIT License
•25•170•15•5•Updated Feb 7, 2025Feb 7, 2025
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•32•48•41•10•Updated Feb 7, 2025Feb 7, 2025
spatialdata-notebooks
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•19•41•5•1•Updated Feb 7, 2025Feb 7, 2025
spatialdata
Public
An open and interoperable data framework for spatial omics data
Python
•
BSD 3-Clause "New" or "Revised" License
•47•249•191•6•Updated Feb 6, 2025Feb 6, 2025
napari-spatialdata
Public
Interactive visualization of spatial omics data
visualization spatial-analysis napari-plugin napari spatial-omics
Python
•
BSD 3-Clause "New" or "Revised" License
•17•48•53•2•Updated Feb 6, 2025Feb 6, 2025
squidpy_notebooks
Public
Tutorials for Squidpy
Jupyter Notebook
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MIT License
•18•30•6•2•Updated Feb 5, 2025Feb 5, 2025
squidpy
Public
Spatial Single Cell Analysis in Python
data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy
Python
•
BSD 3-Clause "New" or "Revised" License
•88•462•76•7•Updated Feb 5, 2025Feb 5, 2025
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
Python
•
BSD 3-Clause "New" or "Revised" License
•36•226•40•5•Updated Feb 5, 2025Feb 5, 2025
ecosystem-packages
Public
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Python
•
BSD 3-Clause "New" or "Revised" License
•40•20•6•6•Updated Feb 5, 2025Feb 5, 2025
cookiecutter-scverse-instance
Public
Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.
Python
•
BSD 3-Clause "New" or "Revised" License
•2•1•0•2•Updated Feb 5, 2025Feb 5, 2025
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•10•72•21•1•Updated Feb 5, 2025Feb 5, 2025
scanpy
Public
Single-cell analysis in Python. Scales to >1M cells.
data-science machine-learning bioinformatics transcriptomics visualize-data scanpy anndata scverse python
Python
•
BSD 3-Clause "New" or "Revised" License
•613•2k•492•68•Updated Feb 5, 2025Feb 5, 2025
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•15•43•69•5•Updated Feb 4, 2025Feb 4, 2025
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•0•1•0•Updated Feb 4, 2025Feb 4, 2025
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•13•15•13•5•Updated Feb 4, 2025Feb 4, 2025
governance
Public
Governance docs for scverse
governance scverse
BSD 3-Clause "New" or "Revised" License
•0•7•19•2•Updated Feb 4, 2025Feb 4, 2025
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•0•2•3•1•Updated Feb 4, 2025Feb 4, 2025
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•118•196•15•1•Updated Feb 4, 2025Feb 4, 2025
anndata
Public
Annotated data.
data-science machine-learning bioinformatics transcriptomics scanpy anndata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•157•600•199•52•Updated Feb 4, 2025Feb 4, 2025
scvi-tutorials
Public
Notebooks used in scvi-tools tutorials
scvi-tools scverse tutorial
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•28•51•8•6•Updated Feb 3, 2025Feb 3, 2025
simple-scvi
Public
Simple scVI implementation
Python
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BSD 3-Clause "New" or "Revised" License
•4•10•0•2•Updated Feb 3, 2025Feb 3, 2025
pytometry
Public
Flow & mass cytometry analytics.
Python
•
Apache License 2.0
•8•43•11•1•Updated Feb 3, 2025Feb 3, 2025
genomic-features
Public
Genomic Features in Python from BioConductor's AnnotationHub
genomics python
Python
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BSD 3-Clause "New" or "Revised" License
•6•20•19•8•Updated Feb 3, 2025Feb 3, 2025
formulaic-contrasts
Public
Build contrasts for models defined with formulaic
Python
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BSD 3-Clause "New" or "Revised" License
•1•11•2•1•Updated Feb 3, 2025Feb 3, 2025
plotting_api
Public
Experimenting with a simplified plotting API for scanpy/scirpy
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•3•2•Updated Feb 3, 2025Feb 3, 2025
muon
Public
muon is a multimodal omics Python framework
muon scrna-seq multi-omics multimodal-data cite-seq scanpy scatac-seq anndata multimodal-omics-analysis mudata
Python
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BSD 3-Clause "New" or "Revised" License
•31•225•38•5•Updated Jan 30, 2025Jan 30, 2025
scverse.github.io
Public
scverse.org website
SCSS
•6•1•16•2•Updated Jan 28, 2025Jan 28, 2025